Directory SEQ_QUALITY/

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westram 2023-07-04 12:14 Rev.: 19425

* reintegrates 'ali' into 'trunk'
- refactorings + fixes related to SEQ_QUALITY + HELIX
* adds: log:branches/ali@19407:19424

116 lines of code changed in 6 files:

• SEQ_QUALITY: SQ_GroupData.cxx (-12), SQ_GroupData.h (-19), SQ_functions.cxx (+60 -86), SQ_functions.h (+2 -2), SQ_helix.h (+6 -17), SQ_main.cxx (+48 -24)

westram 2023-06-25 16:57 Rev.: 19410

* automatically add changekeys for keys generated by calculating sequence quality.
- add 'evaluation' (=result) as last field.

53 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+53 -1)

westram 2023-06-25 16:54 Rev.: 19409

* mostly cosmetic changes to SEQ_QUALITY:
- compact else-if cascades.
* avoid using {{{abs()}}} repeatedly in cascades
- unwrap lines.
- use {{{GB_end_transaction}}}.
- whitespace fixes.

106 lines of code changed in 8 files:

• SEQ_QUALITY: SQ_ambiguities.cxx (+1 -2), SQ_ambiguities.h (+1 -1), SQ_functions.cxx (+88 -264), SQ_functions.h (+7 -7), SQ_helix.h (+6 -6), SQ_main.cxx (+1 -1), SQ_physical_layout.h (+1 -2), seq_quality.h (+1 -1)

westram 2023-06-25 16:30 Rev.: 19407

* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406

17 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_helix.h (+17 -12)

westram 2023-06-15 15:31 Rev.: 19393

* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392

19 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_helix.h (+19 -17)

westram 2022-08-03 15:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

7 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+7 -15)

westram 2022-03-04 16:20 Rev.: 18964

* remove parameter {{{fallback2default}}} from
- {{{create_selection_list}}}
- {{{create_list}}}
- {{{awt_create_TREE_selection_list}}}
- {{{awt_create_CONFIG_selection_list}}}
- {{{awt_create_SAI_selection_list}}}
* remove some - now unused - locals.

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+1 -1)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

2 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+2)

westram 2021-09-15 13:52 Rev.: 18730

* remove trailing whitespace from c source.

4 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_GroupData.h (+1 -1), SQ_ambiguities.h (+1 -1), SQ_functions.cxx (+2 -2)

westram 2021-09-15 13:39 Rev.: 18725

* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

5 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+5 -5)

westram 2021-09-15 13:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+1 -5)

westram 2021-08-17 15:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

3 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+3 -4)

westram 2019-04-01 17:41 Rev.: 17724

* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

2 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+2)

westram 2018-07-23 16:52 Rev.: 17262

* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

6 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (-5), SQ_functions.h (-2), SQ_main.cxx (+6 -1)

westram 2018-06-15 13:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

4 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+3 -3), SQ_main.cxx (+1 -1)

westram 2017-11-28 19:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

4 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_GroupData.h (+3 -3), SQ_helix.h (+1 -2)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

33 lines of code changed in 5 files:

• SEQ_QUALITY: SQ_GroupData.h (+1 -1), SQ_ambiguities.h (+4 -4), SQ_functions.cxx (+15 -15), SQ_helix.h (+7 -7), SQ_main.cxx (+6 -6)

westram 2017-11-06 14:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

2 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_GroupData.h (+2 -2)

westram 2017-07-10 12:29 Rev.: 16119

* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

4 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+4 -1)

westram 2017-01-04 18:06 Rev.: 15513

* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_GroupData.h (+1 -1)

westram 2016-08-17 20:39 Rev.: 15198

* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_GroupData.h (+1 -1)

westram 2016-08-11 11:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

4 lines of code changed in 2 files:

• SEQ_QUALITY: Makefile (+3), SQ_functions.cxx (+1 -1)

westram 2016-07-14 14:45 Rev.: 15053

* merge most WINDOW patches from 'color' into 'trunk'
- color-ranges (completes implementation of #682)
* new types (cyclic, planar and spatial)
* can display as canvas-overlay
* setup in separate window
* allow external access via ID (query, activate)
* adds: log:branches/color@14984,14986:14987,14989,14993,15000,15005:15006,15008,15011,15036

1 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+1)

westram 2016-04-16 14:52 Rev.: 14731

* mark code binding callbacks to non-button-widgets (probably incomplete; see #559 for details)

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_GroupData.cxx (+1 -1)

westram 2015-11-04 10:57 Rev.: 14453

* do not cast AW_POPDOWN

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+1 -1)

westram 2015-10-28 19:12 Rev.: 14434

* use typed callbacks in AWTI, PRIMER_DESIGN, SEQ_QUALITY and REFENTRIES

7 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+7 -8)

westram 2015-07-31 16:15 Rev.: 14118

* added {{{awt_create_filter_awars}}}
- made all awars 'tmp' (saving them did not work)

19 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+19 -24)

westram 2015-04-11 11:10 Rev.: 13705

* add config-manager to sequence quality

23 lines of code changed in 2 files:

• SEQ_QUALITY: Makefile (+1), SQ_main.cxx (+22 -3)

westram 2015-03-29 12:47 Rev.: 13625

* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

27 lines of code changed in 4 files:

• SEQ_QUALITY: Makefile (+2), SQ_functions.cxx (+16 -16), SQ_functions.h (+4 -5), SQ_main.cxx (+5 -4)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+1 -1)

westram 2014-08-14 12:18 Rev.: 12757

* unify selectionlist creator names
* awt_create_selection_list_on_pt_servers
- remove param 'popup', instead split into two function (button and list) as done for SAIs

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+1 -1)

westram 2014-05-13 10:49 Rev.: 12225

* pass 'fallback2default' down into awt_create_selection_list_on_trees()

1 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+1 -1)

westram 2014-04-30 14:36 Rev.: 12138

* reintegrates 'fix' into 'trunk'
- fixes #522
* adds:
- log:branches/fix@12058:12137

52 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+52 -49)

westram 2014-01-28 18:13 Rev.: 11512

* merge [11502,11504,11505] from 'dist' into 'trunk'
* adds:
- log:branches/dist@11502,11504:11505

4 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_main.cxx (+3 -4), seq_quality.h (+1 -1)

westram 2013-12-26 13:48 Rev.: 11401

* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

3 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+3 -5)

westram 2013-11-29 10:32 Rev.: 11261

* use awt_create_select_filter_win() as typed callback
* removed superfluous struct keyword
* renamed some variables ('cd'-ex)

3 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+3 -3)

westram 2013-11-27 19:55 Rev.: 11248

- need cb.h in awt_sel_boxes.hxx

0 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (-1)

westram 2013-11-02 17:41 Rev.: 11034

* depends for [11033]

2 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+2)

westram 2013-10-31 18:14 Rev.: 11007

* prototype for GBK_terminate differed between arb_core.h and arb_msg.h

1 lines of code changed in 1 file:

• SEQ_QUALITY: Makefile (+1)

westram 2013-10-31 16:40 Rev.: 11002

* 'class { public' -> struct

33 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_GroupData.h (+8 -7), SQ_helix.h (+15 -15), SQ_physical_layout.h (+10 -10)

(227 more)